Targeted antibody technologies have advanced the treatment of cancer. For example, cancer immunotherapies involving antibody-drug targets have improved targeted cancer cell killing. Cancer vaccines used to engender a targeted T cell response have met with more limited success. In all cases, the therapies are rarely curative. At least some of the modest efficacy can be attributed to lack of highly effective targets.
Adoptive Cell Transfer (ACT) is one of the most potent approaches to cancer immunotherapy due to its direct enhancement of T cell killing. Recently, the curative potential of ACT has been demonstrated clinically in leukemia and melanoma. Tumor infiltrating lymphocytes (TIL) (a source of tumor-reactive T cells) have been harvested for ACT, expanded and transferred back to patients to increase the number of tumor-reactive T cells. The antigens TIL recognize are unidentified, but presumed to be tumor related. This approach has achieved durable regression in some patients (about 20% of patients on average), but not in the majority of those treated. The TIL repertoire can be refined by selectively expanding a T cell population using one or more antigens to stimulate specific sub-populations of T cells before transfer.
Ideally, a cancer therapy should eliminate a cancer's regeneration-capable cells (C-RC) to achieve the best possibility for durable regression. The use of ACT is severely limited for most solid cancers because of the inability to direct enhanced T cell killing to biologically-relevant tumor markers, i.e., proteins essential to the recurrence of the cancer. These proteins enable the cancer cells to survive and regenerate the cancer. ACT that targets a tumor's C-RC is particularly needed in cancers of vital organs, where complete ablation of a normal, functionally critical cell type is not feasible. ACT is also one of the most promising options for the treatment of late-stage metastatic cancers but most likely only if high probability, high potency, high specificity T-cell antigens can be identified within proteins essential to regenerative capacity. While the use if TIL increases the opportunity for relevant tumor reactivity, its ultimate effectiveness is limited by lack of peptide antigens (Ag) with high curative potential, high potency and high probability (collectively denoted as “HP”) of T cell recognition (HP-Ag).
Tumor-reactive TIL may be used to discover antigenic tumor protein targets. However, this is laborious and the TIL approach to target discovery has several drawbacks that limit the discovery of HP-Ag. Methods that rely on a patients' immune response to identify T cell epitopes can be highly individualized and can miss many potentially valuable antigens. In many patients the immune system has gone through countless refinements and insults leading to a skewed, less than optimal and often ineffective response. Inherent selection of antigen by an individual's immune system is a major drawback to the development of HP ACT (HP-ACT) because of its bias towards certain antigens that may be naturally dominant but not useful for killing the C-RC.
The presence of reactive TILs in patients that have advanced cancer indicates that mere T cell recognition within the tumor is not enough. Aside from supporting the immune response with T cell checkpoint blockade or the use of interleukins, there must be an adequate number of T cells within the tumor or in the circulation. While this is something that ACT can achieve, for it to be an HP-ACT therapy, at least some of these T cells must respond to at least one peptide antigen that is pivotal to the C-RC phenotype.
The fact that targeting a pivotal protein essential for perpetuation of the cancer is the way to achieve a reliable, durable response in solid tumors has gone unrecognized. The lead author of a recent detailed genomic analysis on the “non-Darwinian evolution” of a tumor's mutational landscape concluded that a cancer should be nearly impossible to eliminate with a single target due to extremely high genetic diversity (Ling et al., Proc Nat Acad Sci USA., 112(47):E6496 (2015)). However what has gone unappreciated is that, while this is true for most mutations, it will not be true for proteins essential to regeneration of the cancer, i.e., those pivotal to the C-RC. Irrespective of the complex and differing mutational landscape in each individual, there are proteins pivotal to perpetuation and the C-RC that are likely to be shared by genetic subtypes of cancer. If one can target those pivotal proteins involved in key pathways that are needed for the type of cancer to persist and use it an effective modality like ACT, then it creates the opportunity to eliminate the cancer using a single or a minimal number of targets. There are additional practical advantages to targeting a protein responsible for a key oncogenic pathway: it means that expression of the protein is more likely to be one that persists as the tumor progresses and metastasizes. This is evidenced in the expression of at least two HP-TP proteins (AKAP4 and TMPRSS2-ERG) described herein, In addition, if the C-RC driver is lost due to mutation, the likelihood is that those cancer cells will have evolved into something less lethal, if they survive at all. Using ACT as the modality targeted to the C-RC will eliminate the cancer before it has an opportunity to develop resistant/alternative clones as seen in response to targeted drugs or immune therapies that leave the C-RC behind. Therefore the combination of a C-RC target and the modality deliver the therapy's high curative potential. Methods used to discover epitopes as presented in antigen presenting cells (APC), such as dendritic cells, fail to fully consider the connective steps required to move an immune response from APC and antigen digest to presentation and activation of effector T cells. In many patients these steps are flooded with irregularities from previous treatments and immune regulators leading to a lower probability of epitope effectiveness. These methods do not evaluate the value of the protein associated with the target up front leading to a large amount of work for data that may be of low curative value. Solely genomic methodologies do not necessarily capture the exome and may be limited by pre- and post-transcriptional regulation, making epitope evaluation of little translatable value without substantial further investigation. Strictly screening stem cell exomes, either genomic or proteomic, limits targets to normal developmental or proliferative antigens and may miss mutation-, translocation-derived or novel expressed antigens, Moreover, most proliferative or metabolic antigens are likely conserved and in use in normal tissue turnover.
Genomic screens with limited additional expression patterning analysis can lead to simple overexpression candidates. This is exemplified by the studies of Ochsenreither, et al. (Ochsenreither, et al. Blood 119(23):5492-5501 (2012)) where, after a large effort, Cyclin-A1 presented as a viable target, yet, the normal expression pattern of Cyclin-A1 makes it a poor target, highly susceptible to off-target responses or possibly normal immune regulatory diminution of the response. Multiplatform analyses based on primarily genomic (Hoadley, et al. Cell 158(4):929-944 (2014)) data have been performed with relatively predictable results uncovering genetic mutations and amplifications clustered in well-known pathways such as p53 and PI3kinase within the subtypes these categorize. There remains a need for methods for identifying T cell epitopes that target cells capable of regenerating cancers, and hence have curative potential.
It is therefore an object of the present invention to provide a method for identifying T-cell epitopes which target cells capable of regenerating cancers.
It is also an object of the present invention to provide epitopes with a high curative potential, high potency and high probability of T cell recognition.
It is still an object of the present invention to provide methods and systems for programming T cells to selectively attack important tumor cells involved in proliferation, or invasion in an individual.